data_6993 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Phosphorylation of Cytoplasmic Tail of Tissue Factor and its Role in Modulating Structure and Binding Affinity. ; _BMRB_accession_number 6993 _BMRB_flat_file_name bmr6993.str _Entry_type original _Submission_date 2006-02-17 _Accession_date 2006-02-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; This peptide has two chemically modified amino acids(phosphorylated), Ser253 and Ser258 ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sen Mehmet . . 2 Agrawal Sameer . . 3 Craft John . . 4 Ruf Wolfram . . 5 Legge Glen B. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 103 "13C chemical shifts" 33 "15N chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-09-13 update BMRB 'update entry citation' 2007-06-20 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 6991 'unphosphorylated varian of Tissue Factor Cytoplasmic Domain' 6996 'Single 253 phosphorylated variant of Tissue Factor Cytoplasmic Domain' 6998 'Single 258 phosphorylated variant of Tissue Factor Cytoplasmic Domain' 7118 'Neurabin SAM domain monomer' stop_ _Original_release_date 2006-02-17 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Spectroscopic Characterization of Successive Phosphorylation of the Tissue Factor Cytoplasmic Region ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20076769 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sen Mehmet . . 2 Herzik Mark . . 3 Craft John W. . 4 Creath Andrea L. . 5 Agrawal Sameer . . 6 Ruf Wolfram . . 7 Legge Glen B. . stop_ _Journal_abbreviation 'Open Spectrosc J.' _Journal_name_full 'The open spectroscopy journal' _Journal_volume 3 _Journal_issue . _Journal_ISSN 1874-3838 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 58 _Page_last 64 _Year 2009 _Details . loop_ _Keyword 'Homonuclear NMR' NMR 'Tissue Factor' phosphorylation stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name TFPP _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'TFPP, trans conformer' $Tissue_Factor_Cytoplasmic_Domain 'TFPP, cis conformer' $Tissue_Factor_Cytoplasmic_Domain stop_ _System_molecular_weight 2218.3 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'all free' loop_ _Biological_function 'Cell signaling' stop_ _Database_query_date . _Details 'Synthetic Peptide of the Double Phosphorylated Tissue Factor Cytoplasmic Domain (TFPP)' save_ ######################## # Monomeric polymers # ######################## save_Tissue_Factor_Cytoplasmic_Domain _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TFPP _Molecular_mass 2218.3 _Mol_thiol_state 'all free' loop_ _Biological_function 'Cell Signaling' stop_ _Details 'Cis conformation of the Pro259 was assigned.' ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence ; CRKAGVGQXWKENXPLNVS ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 245 CYS 2 246 ARG 3 247 LYS 4 248 ALA 5 249 GLY 6 250 VAL 7 251 GLY 8 252 GLN 9 253 SEP 10 254 TRP 11 255 LYS 12 256 GLU 13 257 ASN 14 258 SEP 15 259 PRO 16 260 LEU 17 261 ASN 18 262 VAL 19 263 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_SEP _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common PHOSPHOSERINE _BMRB_code . _PDB_code SEP _Standard_residue_derivative . _Molecular_mass 185.072 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Sep 28 18:48:16 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? OG OG O . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? P P P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O3P O3P O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HXT HXT H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB OG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING OG P ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? DOUB P O1P ? ? SING P O2P ? ? SING P O3P ? ? SING O2P HOP2 ? ? SING O3P HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Tissue_Factor_Cytoplasmic_Domain Human 9606 Eukaryota Metazoa Homo sapiens stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $Tissue_Factor_Cytoplasmic_Domain 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 6mM TFPP in 10% D2O pH 6.0 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Tissue_Factor_Cytoplasmic_Domain 6 mM . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Task 'NMRView was used for Assignment' stop_ _Details 'Johnson et al. Methods Mol. Bio. 2004' save_ save_nmrpipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Task 'NMR data Processing' stop_ _Details 'Delaglio et al J. Biomol. NMR 1995' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details '800 and 600 MHz Bruker Avance spectrometers are used to acquire data' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details '800 and 600 MHz Bruker Avance spectrometers are used to acquire data' save_ ############################# # NMR applied experiments # ############################# save_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_IP-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name IP-COSY _Sample_label $sample_1 save_ save_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _Sample_label $sample_1 save_ save_1H1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name 1H1H_NOESY _Sample_label $sample_1 save_ save_1H15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name 1H15N_HSQC _Sample_label $sample_1 save_ save_1H13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name 1H13C_HSQC _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_conditions_of_TFPP _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 0 mM pH 6.0 0.05 pH pressure 1 0 atm temperature 285 0.3 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_TMS _Saveframe_category chemical_shift_reference _Details ; Carbon and Nitrogen dimension was referenced based of gyromagnetic ratio relativity of these nuclei and proton. ; loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio TMS C 13 'methyl protons' ppm 0 external indirect . 'outside sample' . 0.251449520 TMS H 1 'methyl protons' ppm 0 external direct cylindrical 'outside sample' . 1.0 TMS N 15 'methyl protons' ppm 0 external indirect . 'outside sample' . 0.101329050 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $NMRView $nmrpipe stop_ loop_ _Experiment_label ROESY IP-COSY TOCSY 1H15N_HSQC 1H13C_HSQC stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $conditions_of_TFPP _Chem_shift_reference_set_label $TMS _Mol_system_component_name 'TFPP, trans conformer' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 247 3 LYS H H 8.50 0.02 1 2 247 3 LYS HA H 4.14 0.02 1 3 247 3 LYS HB2 H 1.66 0.02 2 4 247 3 LYS HB3 H 1.55 0.02 2 5 247 3 LYS HG2 H 1.28 0.02 1 6 247 3 LYS HG3 H 1.28 0.02 1 7 247 3 LYS CA C 56.2 0.10 1 8 247 3 LYS CB C 33.3 0.10 1 9 247 3 LYS CG C 24.8 0.10 1 10 247 3 LYS N N 124.2 0.10 1 11 248 4 ALA H H 8.39 0.02 1 12 248 4 ALA HA H 4.15 0.02 1 13 248 4 ALA HB H 1.24 0.02 1 14 248 4 ALA CA C 52.4 0.10 1 15 248 4 ALA CB C 19.5 0.02 1 16 248 4 ALA N N 126.1 0.10 1 17 249 5 GLY H H 8.25 0.02 1 18 249 5 GLY HA2 H 3.83 0.02 1 19 249 5 GLY HA3 H 3.83 0.02 1 20 249 5 GLY N N 108.7 0.02 1 21 250 6 VAL H H 8.04 0.02 1 22 250 6 VAL HA H 4.06 0.02 1 23 250 6 VAL HB H 2.00 0.02 1 24 250 6 VAL HG1 H 0.81 0.02 2 25 250 6 VAL HG2 H 0.81 0.02 2 26 250 6 VAL CA C 62.3 0.10 1 27 250 6 VAL CB C 32.7 0.10 1 28 250 6 VAL N N 125.1 0.10 1 29 251 7 GLY H H 8.70 0.02 1 30 251 7 GLY HA2 H 3.86 0.02 2 31 251 7 GLY HA3 H 3.93 0.02 2 32 251 7 GLY CA C 45.2 0.10 1 33 251 7 GLY N N 113.5 0.10 1 34 252 8 GLN H H 8.20 0.02 1 35 252 8 GLN HA H 4.24 0.02 1 36 252 8 GLN HB2 H 1.92 0.02 2 37 252 8 GLN HB3 H 1.80 0.02 2 38 252 8 GLN HG2 H 2.17 0.02 1 39 252 8 GLN HG3 H 2.17 0.02 1 40 252 8 GLN HE21 H 6.82 0.02 2 41 252 8 GLN HE22 H 7.52 0.02 2 42 252 8 GLN CA C 55.7 0.10 1 43 252 8 GLN CG C 33.7 0.10 1 44 252 8 GLN N N 119.4 0.10 1 45 252 8 GLN NE2 N 112.9 0.10 1 46 253 9 SEP H H 8.99 0.02 1 47 253 9 SEP HA H 4.35 0.02 1 48 253 9 SEP HB2 H 3.99 0.02 1 49 253 9 SEP N N 118.0 0.10 1 50 253 9 SEP CA C 58.0 0.10 1 51 253 9 SEP CB C 65.6 0.10 1 52 254 10 TRP H H 8.13 0.02 1 53 254 10 TRP HA H 4.50 0.02 1 54 254 10 TRP HB2 H 3.16 0.02 1 55 254 10 TRP HB3 H 3.16 0.02 1 56 254 10 TRP HD1 H 7.18 0.02 1 57 254 10 TRP HE1 H 10.1 0.02 1 58 254 10 TRP HE3 H 7.46 0.02 1 59 254 10 TRP HZ2 H 7.39 0.02 1 60 254 10 TRP HZ3 H 7.03 0.02 1 61 254 10 TRP HH2 H 7.12 0.02 1 62 254 10 TRP CA C 57.5 0.10 1 63 254 10 TRP CB C 29.5 0.10 1 64 254 10 TRP N N 120.6 0.10 1 65 254 10 TRP NE1 N 129.8 0.10 1 66 255 11 LYS H H 7.79 0.02 1 67 255 11 LYS HA H 4.07 0.02 1 68 255 11 LYS HB2 H 1.55 0.02 2 69 255 11 LYS HB3 H 1.46 0.02 2 70 255 11 LYS HG2 H 1.08 0.02 1 71 255 11 LYS HG3 H 1.08 0.02 1 72 255 11 LYS HD2 H 1.54 0.02 1 73 255 11 LYS HD3 H 1.54 0.02 1 74 255 11 LYS HE2 H 2.90 0.02 1 75 255 11 LYS HE3 H 2.90 0.02 1 76 255 11 LYS CA C 55.6 0.10 1 77 255 11 LYS CB C 33.6 0.10 1 78 255 11 LYS CG C 24.312 0.10 1 79 255 11 LYS CE C 42.1 0.10 1 80 255 11 LYS N N 123.7 0.10 1 81 256 12 GLU H H 8.16 0.02 1 82 256 12 GLU HA H 4.01 0.02 1 83 256 12 GLU HB2 H 1.79 0.02 2 84 256 12 GLU HB3 H 1.91 0.02 2 85 256 12 GLU HG2 H 2.17 0.02 1 86 256 12 GLU HG3 H 2.17 0.02 1 87 256 12 GLU CA C 56.3 0.10 1 88 256 12 GLU CG C 36.0 0.10 1 89 257 13 ASN H H 8.44 0.02 1 90 257 13 ASN HA H 4.85 0.02 1 91 257 13 ASN HB2 H 2.63 0.02 2 92 257 13 ASN HB3 H 2.73 0.02 2 93 257 13 ASN HD21 H 7.62 0.02 2 94 257 13 ASN HD22 H 6.88 0.02 2 95 257 13 ASN CA C 53.3 0.02 1 96 257 13 ASN N N 120.2 0.10 1 97 257 13 ASN ND2 N 113.4 0.10 1 98 258 14 SEP H H 8.66 0.02 1 99 258 14 SEP HA H 4.69 0.02 1 100 258 14 SEP HB2 H 3.89 0.02 2 101 258 14 SEP HB3 H 3.99 0.02 2 102 258 14 SEP N N 118.6 0.10 1 103 258 14 SEP CA C 55.8 0.10 1 104 258 14 SEP CB C 65.1 0.10 1 105 259 15 PRO HA H 4.28 0.02 1 106 259 15 PRO HB2 H 1.69 0.02 2 107 259 15 PRO HB3 H 1.50 0.02 2 108 259 15 PRO HG2 H 1.64 0.02 1 109 259 15 PRO HG3 H 1.64 0.02 1 110 259 15 PRO HD2 H 3.69 0.02 2 111 259 15 PRO HD3 H 3.63 0.02 2 112 259 15 PRO CB C 32.1 0.10 1 113 259 15 PRO CG C 27.4 0.10 1 114 259 15 PRO CD C 50.7 0.10 1 115 260 16 LEU H H 8.35 0.02 1 116 260 16 LEU HA H 4.20 0.02 1 117 260 16 LEU HB2 H 1.54 0.02 1 118 260 16 LEU HB3 H 1.54 0.02 1 119 260 16 LEU HG H 1.47 0.02 1 120 260 16 LEU HD1 H 0.83 0.02 1 121 260 16 LEU HD2 H 0.83 0.02 1 122 260 16 LEU CA C 55.16 0.10 1 123 260 16 LEU CB C 42.39 0.10 1 124 260 16 LEU N N 122.1 0.10 1 125 261 17 ASN H H 8.43 0.02 1 126 261 17 ASN HA H 4.65 0.02 1 127 261 17 ASN HB2 H 2.63 0.02 2 128 261 17 ASN HB3 H 2.73 0.02 2 129 261 17 ASN HD21 H 7.62 0.02 2 130 261 17 ASN HD22 H 6.88 0.02 2 131 261 17 ASN CA C 53.1 0.02 1 132 261 17 ASN N N 120.2 0.10 1 133 261 17 ASN ND2 N 113.5 0.10 1 134 262 18 VAL H H 8.14 0.02 1 135 262 18 VAL HA H 4.15 0.02 1 136 262 18 VAL HB H 2.06 0.02 1 137 262 18 VAL HG1 H 0.83 0.02 2 138 262 18 VAL HG2 H 0.83 0.02 2 139 262 18 VAL CA C 62.0 0.10 1 140 262 18 VAL CB C 32.9 0.10 1 141 262 18 VAL N N 119.0 0.10 1 142 263 19 SER H H 8.00 0.02 1 143 263 19 SER HA H 4.19 0.02 1 144 263 19 SER HB2 H 3.76 0.02 1 145 263 19 SER HB3 H 3.76 0.02 1 146 263 19 SER CA C 60.0 0.10 1 147 263 19 SER CB C 64.7 0.02 1 stop_ save_ save_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $NMRView $nmrpipe stop_ loop_ _Experiment_label ROESY IP-COSY TOCSY 1H15N_HSQC 1H13C_HSQC stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $conditions_of_TFPP _Chem_shift_reference_set_label $TMS _Mol_system_component_name 'TFPP, cis conformer' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 259 15 PRO HA H 4.78 0.02 1 2 259 15 PRO HB2 H 3.47 0.02 1 3 259 15 PRO HB3 H 2.31 0.02 1 4 259 15 PRO HG2 H 2.03 0.02 1 5 259 15 PRO HG3 H 1.87 0.02 1 6 259 15 PRO HD2 H 1.75 0.02 1 7 259 15 PRO HD3 H 1.75 0.02 1 stop_ save_